If everything was working fine until you swapped in a new motherboard and everything else is the same as before, then I think youve found your culprit and it might be time to RMA. The power switch is pretty much idiot proof and will only fit on the header one way. Besides, if you hooked it up to the wrong header, it wouldnt even be turning on at all.

I know its the most obvious choice. Hence my post in the mobo forum I would like to try to understand as to why it works sometimes and other times it doesn't.

What part of the mobo controls that side? I guess I want to get my ducks in a row for when I call Asus. Its a little annoying that I'll have to RMA this board, meaning i'll be without it for a couple of weeks